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log of Clinical Decision Support telecon 14 Jun 2012

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 21 Jun 2012 11:14:03 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20120621151402.GE30664b@w3.org>
I forgot to send these to the list last week. Apologies.



                                   - DRAFT -


14 Jun 2012

   See also: [2]IRC log





     * [3]Topics
         1. [4]Medicine Safety Code project
         2. [5]simon_lin intro
     * [6]Summary of Action Items

   <matthias_samwald> argh

   <scribe> scribenick: ericP

Medicine Safety Code project

   matthias_samwald: presented a few months ago at AMIA
   ... BobF and simon_lin were there
   ... how do we give pharmacogenomic data to clinicians without too many
   privacy or centralization issues?

   <matthias_samwald> [7]http://safety-code.org/

   matthias_samwald: also sidestepping the sluggish uptake of EHRs
   ... QR-code with the ~400 SNPs of most pharmacogenomic interest
   ... populated by microarrays or nextgen
   ... QR-code points a URL
   ... avoiding centralization
   ... genetic data is associated with many privacy issues:
   ... .. (personal) genetic data
   ... .. serves as a genetic fingerprint


   matthias_samwald: law in Austria avoids genetic data

   simon_lin: this URL includes the data

   matthias_samwald: exactly, ~250 chars. can be carried with you

   BobF: so your URL will decode the data and present the info

   matthias_samwald: yes
   ... you can interpret such a medicine safety code can be interpreted by
   most phones

   BobF: but your server is responsible for keeping the guidelines up to
   ... that's not a trivial task

   matthias_samwald: indeed. so far just a research datatype

   <BobF> ericP - the questions were from BobF (not BobF) :-)


   simon_lin: given your compression, how much info can you put in?
   ... i assume the size of the QRcode is a design constraint

   matthias_samwald: putting lots of data in a code makes it very complex
   and hard to scan

   BobF: how many can you fit now?

   matthias_samwald: i'm fitting ~400 SNPs. can't exceed ~800 with current

   ericP: this is good for 5 years?

   matthias_samwald: around 10 probably

   boycer: you've got a good set of phase I/phase II
   ... pharmacodynamics is what your body does
   ... there are a hand-full of enzymes for phase I (oxidizing/reducing)
   ... pharmacokinetics won't change much over the next years


   boycer: but pharmacodynamics will explode over the next few years
   ... it's easier to predict pharmacokinetics
   ... but e.g. statin doesn't have a clear safe range

   matthias_samwald: the 400 i use were compiled from the PharmGKB "VIP"
   genes (those with existing clinical evidence)
   ... combined with a list from pharma adne (SP?)
   ... added also those listed in FDA drug labels

   <boycer> Matthias - what was the pharma database (I heard Pharma ad &


   <boycer> Found it: www.pharmaadme.org/

   matthias_samwald: pharmacodynamics would seem more interesting than
   pharmacokinetics, but the latter are further along
   ... CPIC SNPs are primarily kinetic

   BobF: we're working on a schema for conveying guidelines which can be
   hooked into a clinical support engine
   ... could you use that to update safety-code.org?


   matthias_samwald: that'd be helpful
   ... in the last few days, i've updated this spreadsheet with CPIC and
   Dutch Pharmacogenomics WG guidelines from PharmaGKB
   ... i'd like to further curate the data to create CDS rules in SPARQL
   ... but it would be great the have machine-readable CPIC guidelines

   BobF: that's my goal


   ericP: use RDF/XML with controlled schema? GRDDL? conneg?

   matthias_samwald: i think RDF/XML is the worst of both worlds
   ... the rows in the spreadsheet represent multiple SNP combos
   ... we can break up some of the CPIC guidelines in this table into
   smaller rows

   BobF: i didn't intend to create a comprehensive pharmacogenomics domain
   ... just serialize CPIC guidelines
   ... there are national efforts in the US to create generic CDS rules
   ... i'd like to link the schema to those rules so there's a path from
   the CPIC guidelines to what the hospitals can implement

   ericP: how complex are these rules?

   <matthias_samwald> example of guideline and boolean logic:

   BobF: most are single drug/geneotype combo
   ... warfarin is the most complex with a 2X2 matrix

   <matthias_samwald> bite tge second row in the second table.

   <matthias_samwald> note the second row in the second table

   BobF: as we apply more systems bio, this will get more complex
   ... need to distinguish between broad clinical practics and specific
   ... each institution will have to decide the latter

   ericP: would you want your expressivity to cover quatitative dosing
   even though you're not using all of that expressivity?

   BobF: i'd like it to be extensible but i can't populate it now

   matthias_samwald: the more complex the expressivity, the harder it is
   for clinicians to understand and the harder it is to validate

   boycer: is the safety-code.org infrastructure going to be public?

   matthias_samwald: it's a jenna back-end and i'll make the SPARQL rules

simon_lin intro

   UNKNOWN_SPEAKER: we're doing a trial looking at 80 genes via nextgen
   ... we're analyzing the impact of markers to see how we can change our
   ... marshfield clinic also has an insurance subsidiary
   ... we'd like to put medicine safety codes and drug interactions into
   an insurance card
   ... Mayo clinic and about 8 participants in Emerge
   ... expect recruitment next year



Summary of Action Items

   [End of minutes]

    Minutes formatted by David Booth's [15]scribe.perl version 1.136
    ([16]CVS log)
    $Date: 2012/06/14 16:08:59 $

Scribe.perl diagnostic output

   [Delete this section before finalizing the minutes.]
This is scribe.perl Revision: 1.136  of Date: 2011/05/12 12:01:43
Check for newer version at [17]http://dev.w3.org/cvsweb/~checkout~/2002/scribe/

Guessing input format: RRSAgent_Text_Format (score 1.00)

FAILED: s/boyver/BobF/g
Succeeded: s/boycer/BobF/g
Succeeded: s/pharmacogenetics/pharmacokinetics/
Succeeded: s/put SNPs and drug interactions/put medicine safety codes and drug i
Found ScribeNick: ericP
Inferring Scribes: ericP

WARNING: No "Present: ... " found!
Possibly Present: BobF MacTed P15 Tony aaaa aabb boycer data egonw ericP https m
atthias_samwald scribenick simon_lin
You can indicate people for the Present list like this:
        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy

WARNING: No meeting title found!
You should specify the meeting title like this:
<dbooth> Meeting: Weekly Baking Club Meeting

WARNING: No meeting chair found!
You should specify the meeting chair like this:
<dbooth> Chair: dbooth

Got date from IRC log name: 14 Jun 2012
Guessing minutes URL: [18]http://www.w3.org/2012/06/14-hcls-minutes.html
People with action items:

   [End of [19]scribe.perl diagnostic output]


   1. http://www.w3.org/
   2. http://www.w3.org/2012/06/14-hcls-irc
   3. http://www.w3.org/2012/06/14-hcls-minutes#agenda
   4. http://www.w3.org/2012/06/14-hcls-minutes#item01
   5. http://www.w3.org/2012/06/14-hcls-minutes#item02
   6. http://www.w3.org/2012/06/14-hcls-minutes#ActionSummary
   7. http://safety-code.org/
   8. http://safety-code.org/v0.1/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e56407xu6O0000000000000000000000000000
   9. http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
  10. http://pharmaadme.org/joomla/index.php?option=com_content&task=view&id=12&Itemid=27
  11. https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
  12. http://pharmgkb.org/gene/PA128
  13. https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/About
  14. http://www.w3.org/People/Eric/ericP-foaf
  15. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  16. http://dev.w3.org/cvsweb/2002/scribe/
  17. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
  18. http://www.w3.org/2012/06/14-hcls-minutes.html
  19. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm

Received on Thursday, 21 June 2012 19:58:08 UTC

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